The innovation ability of students is one of the most important objectives that need to be cultivated in colleges and universities. The comprehensive evaluation of innovation ability discussed in the study can be divided into two stages: the first stage can be called preliminary evaluation and its main target is to identify students with innovative potential; in the second stage, the target objects found in the previous stage will be evaluated quantitatively and ranked. However, it is always difficult to quantitatively evaluate the innovation ability by using traditional algorithms. Based on the above analysis, the study proposes an algorithm to quantitatively evaluate the innovation ability with the help of management thought and fuzzy mathematics. Data are the basis of evaluation, and the accuracy of the data directly determines the quality of the algorithm; the data structure of the incompletely probabilistic fuzzy set is proposed in the study; the data structure can fully consider the fuzziness of the problem and the hesitation in the decision-making process; it can save the original detailed data to the maximum extent. Certainly, certain information may be lost or only the value range can be determined; there are usually some unknowns in the evaluation data, and the consistency optimization model is proposed for solving the problem. Usually, there are certain contradictions among the evaluation data; the definition of the consistency degree is proposed in the study; the consistency can be verified in time after all the unknowns are obtained, and the automatic adjustment module will be activated immediately if the value of the consistency degree exceeds the warning threshold. Finally, after verifying the data consistency, the solution can be obtained by solving the optimization model. Several experiments have been carried out to verify the effectiveness and high-discrimination ability of the algorithm proposed in the study; meanwhile, the superiority of the algorithm is further verified through comparisons with other outstanding algorithms.